def _toatoms(self, include_results=False):
if not include_results:
return ase.atoms.Atoms(
self.numbers,
self.positions,
cell=self.cell,
pbc=(self.pbc & np.array([1, 2, 4])).astype(bool),
)
if self.constraints:
constraints = json.loads(self.constraints)
if len(constraints[0]['kwargs']['indices']) > 0:
constraints = [dict2constraint(d) for d in constraints]
else:
constraints = None
atoms = ase.atoms.Atoms(self.numbers,
self.positions,
cell=self.cell,
pbc=(self.pbc
& np.array([1, 2, 4])).astype(bool),
magmoms=self.magmoms,
charges=self.charges,
tags=self.tags,
masses=self.masses,
momenta=self.momenta,
constraint=constraints)
if not self.calculator == "unknown":
params = self.get('calculator_parameters', {})
atoms.calc = get_calculator(self.calculator)(**params)
else:
all_properties = [
'energy', 'forces', 'stress', 'dipole', 'charges', 'magmom',
'magmoms', 'free_energy'
]
results = {}
#print(getattr(self, 'energy'))
for prop in all_properties:
result = getattr(self, prop, None)
if result is not None:
results[prop] = result
# print(results)
if results:
atoms.calc = SinglePointCalculator(atoms, **results)
atoms.calc.name = getattr(self, 'calculator', 'unknown')
atoms.info = {}
atoms.info['unique_id'] = self.unique_id
atoms.info['key_value_pairs'] = self.key_value_pairs
data = self.data
if data:
atoms.info['data'] = data
return atoms
def process_result_value(self, value, dialect):
return json.loads(value)
def _dft_code(self):
return json.loads(self.key_value_pairs).get('dft_code', '')
def _dft_functional(self):
return json.loads(self.key_value_pairs).get('dft_functional', '')
def _facet(self):
return json.loads(self.key_value_pairs).get('facet', '').strip("()")
def _substrate(self):
return json.loads(self.key_value_pairs).get('substrate', '')
def _adsorbate(self):
return json.loads(self.key_value_pairs).get('adsorbate', '')
def _username(self):
return json.loads(self.key_value_pairs).get('username', '')
def _reaction(self):
reaction = json.loads(self.key_value_pairs).get('reaction', '')
reaction = reaction.replace('__', '->').replace('_', '+')
return reaction